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bigbio / proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets
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Discordance in FTP URL in column 10 in sdrf file (comment[associated file uri]) #90

Closed mstephania closed 4 years ago

mstephania commented 4 years ago

In annotation of PXD000612 project does not exist for the following samples:

pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep4_pH11.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep4_pH3.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep4_pH4.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep4_pH5.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep4_pH6.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep4_pH8.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep5_pH11.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep5_pH3.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep5_pH4.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep5_pH5.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep5_pH6.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep5_pH8.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep6_pH11.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep6_pH3.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep6_pH4.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep6_pH5.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep6_pH6.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Control_rep6_pH8.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep1_pH11.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep1_pH3.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep1_pH4.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep1_pH5.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep1_pH6.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep1_pH8.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep2_pH11.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep2_pH3.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep2_pH4.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep2_pH5.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep2_pH6.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep2_pH8.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep3_pH11.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep3_pH3.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep3_pH4.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep3_pH5.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep3_pH6.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep3_pH8.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep4_pH11.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep4_pH3.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep4_pH4.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep4_pH5.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep4_pH6.raw pY_EXQ5_KiSh_SA_LabelFree_HeLa_Proteome_Nocodazole_rep4_pH8.raw

and for the rest of the samples the URL is different e.g.: For 20120309_EXQ5_KiSh_SA_LabelFree_HeLa_Phospho_EGF_rep4_FT3.raw instead of this: ftp://ftp.pride.ebi.ac.uk/pride/archive/projects/PXD000612/20120309_EXQ5_KiSh_SA_LabelFree_HeLa_Phospho_EGF_rep4_FT3.raw it should be this: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/08/PXD000612/20120309_EXQ5_KiSh_SA_LabelFree_HeLa_Phospho_EGF_rep4_FT3.raw

ypriverol commented 4 years ago

Can you @qinchunyuan review this issue.

daichengxin commented 4 years ago

Thanks,This issue has been modified by #96